Apple isn't degrading the speed of home screen web apps. It's boosting the speed of web apps in the browser. But in the long run, the effect is the same. And if this is a bug, Apple has yet to fix it.
In a more disturbing discovery, home screen web apps are reportedly unable to access certain web caches that were present before iOS 4.2.
On top of this, apps are hampered by the cache and asynchronous mode issues. According to one anonymous developer, access to certain web caches was cut off in iOS 4.2. And the issue is confirmed by a second developer. You can try it yourself with HTML5 apps such as Pie Guy. With earlier versions of the OS, if you move the game to the home screen and run it once, you can then play it offline. But if you try to do so on the latest version of the operating system, you can't.
The Register's sources say that Apple is aware of the problem and that the Mobile Safari team has indicated the issues will not be fixed.
Read More [via Samer]